Simulating autosomal genotypes with realistic linkage disequilibrium and a spiked-in genetic effect.

ABSTRACT:

Background

To evaluate statistical methods for genome-wide genetic analyses, one needs to be able to simulate realistic genotypes. We here describe a method, applicable to a broad range of association study designs, that can simulate autosome-wide single-nucleotide polymorphism data with realistic linkage disequilibrium and with spiked in, user-specified, single or multi-SNP causal effects.

Results

Our construction uses existing genome-wide association data from unrelated case-parent triads, augmented by including a hypothetical complement triad for each triad (same parents but with a hypothetical offspring who carries the non-transmitted parental alleles). We assign offspring qualitative or quantitative traits probabilistically through a specified risk model and show that o

SUBMITTER: Shi M 

PROVIDER: S-EPMC5749028 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature